Gastrointestinal stromal tumor (GIST) is the most common type of human sarcomas, arising from the interstitial cells of Cajal (ICCs). The majority of GISTs harbor activating KIT mutations, which is thought to be the main oncogenic drive in GIST pathogenesis. Imatinib is an effective therapy in advanced GISTs. However, resistance invariably develops, and it is imperative to better understand the pathogenesis of GIST and to identify novel therapeutic targets in GIST management. Our preliminary studies show that ETV1, an ETS family transcription factor implicated in the pathogenesis of other malignancies including prostate cancer, is a master regulator of a transcriptional program that characterizes cells belonging to the ICC-GIST lineage and is required for their maintenance and survival. We further show that ETV1 regulates the GIST-signature genes primarily via binding to their cis-regulatory regions/enhancers at the genomic level. Additionally, our studies show that KIT with activating mutations strongly cooperates with ETV1 in tumorigenesis at least in part by stabilizing ETV1 protein levels. Our findings suggest that ETV1 may define the optimal cellular context for KIT- driven oncogenesis in GIST, and provide a rationale for why patients and mice with germ-line activating-KIT mutations exclusively develop neoplasia in the ICC-lineage, but not of other cell lineages that are known to be developmentally regulated by KIT, including melanocytes, germ cells, and hematopoietic cells. These observations led to the following specific aims to further characterize the genomic and epigenomic aspects of ETV1 transcriptional regulation that underlies the cellular context in GIST, to dissect the functional interplay of KIT signaling with ETV1 transcriptional program, and to more rigorously investigate the role of ETV1 in GIST initiation and maintenance, with the goal to better understand GIST pathogenesis and to identify novel strategies for next-generation of targeted therapy in GIST management. I propose to perform genome-wide mapping of ETV1 cistrome and histone modifications characteristic of enhancers and promoters, and integrate with ETV1 transcriptome studies to gain a comprehensive understanding of the genomic and epigenomic regulation of the ETV1 transcriptional program that underlie the cellular context in GIST oncogenesis. Second, I propose to define the downstream KIT pathway involved in regulation of ETV1 protein stability;I also propose to directly assess whether ETV1 transcriptional program is the critical pathway that mediates GIST oncogenesis downstream of activated KIT signaling, using degradation-resistant ETV1 mutants in imatinib rescuing experiments. Third, I propose to use pre-existing GIST and Etv1-knockout mouse models to examine the requirement of ETV1 for initiation and/or maintenance of GIST in vivo. These studies will provide a comprehensive understanding of the pathogenesis of GIST mediated by the ETV1 transcriptional program and can have broad implications on other ETS transcription factor dependent malignancies. As importantly, it will provide a novel therapeutic strategy in imatinib-resistant GIST and likely other ETV1-dependent malignancies. This project will be performed under the joint mentorship of Dr. C. David Allis at the Rockefeller University, a world renowned expert in epigenetics and regulation of transcription, and Dr. Charles L. Sawyers at MSKCC who initially developed imatinib for chronic myelogenous leukemia treatment with tremendous expertise in cell signaling mouse modeling and translational research. During the training period, I will gain proficiency in many areas using diverse techniques to tackle the role of ETV1 in GIST pathogenesis. At the end of the period, my goal is become an independent physician-scientist combining bench based research and clinical care of sarcoma patients. PUBLIC HEALTH RELEVANCE: Despite the effectiveness of tyrosine kinase inhibitors (TKIs), resistance to TKIs has become an increasing clinical problem in the treatment of gastrointestinal stromal tumors (GISTs), and novel therapeutic strategies are imperative. ETV1 is recently discovered by us as a lineage-specific transcription factor that regulates the GIST phenotype and is required for the growth and survival of GIST. Here, I propose to investigate the roles ETV1 in the pathogenesis of GIST using mouse models and genome-wide analyses of the ETV1-mediated transcriptional regulation, and to identify novel therapeutic strategies for TKI-resistant GIST.